We study the impact that the crystal defects have on the $C$-type structure of rare earth sesquioxide thin films grown by ion-beam sputtering, through the example of ${\mathrm{Y}}_{2}$O${}_{3}$. By monitoring the energy of the argon beam used in the sputter deposition process (between 600 and 1200 eV), we show that it is possible to control the microstructure (defects concentration, stress state and phase) in the oxide layer. Two main types of defects, ascribed to the ``atomic peening effect'', are evidenced by high-resolution transmission electron microscopy, Rutherford backscattering spectroscopy, and nuclear reaction analysis experiments: anti-Frenkel pairs, leading to a disorder on the oxygen-vacancy network, and oxygen-vacancy dislocations loops, to accommodate the strong nonstoichiometry. From a macroscopic measurement of the residual stresses in the as-deposited and the annealed layers, through x-ray diffraction and the $\mathrm{sin}{}^{2}\ensuremath{\Psi}$ method, we have modeled the related stress state using an enhanced triaxial stress model. In the as-grown films, we evidence the coexistence of a biaxial and a hydrostatic stress, due to inclusions of atomic size defects. Quantitative information of the concentration and the nature of each type of defect (size effect) have also been determined, in good agreement with experiments. Interestingly, in the most energetic growth conditions corresponding to the highest degree of disorder on the oxygen-vacancy network and to the highest stress field in the film, we demonstrate that it is possible to stabilize an unexpected and metastable non equilibrium fluorite-like phase (X-type).